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Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time [RNA-seq]

ABSTRACT: Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time [RNA-seq]

PROVIDER: PRJNA790958 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17281222.fastq.gz	Fastqsanger.gz
	SRR17281223.fastq.gz	Fastqsanger.gz
	SRR17281224.fastq.gz	Fastqsanger.gz
	SRR17281225.fastq.gz	Fastqsanger.gz
	SRR17281226.fastq.gz	Fastqsanger.gz

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Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time

Project description:Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time

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Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time [BiSulfite-seq]

Project description:Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time [BiSulfite-seq]

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Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time [RNA-seq]

Project description:Cytosine methylation is a reversible epigenetic modification to DNA. In plants, removal of cytosine methylation is accomplished by the four members of the DME family of 5-methylcytosine DNA glycosylases. Demethylation by DME is critical for seed development. Consequently, determining the function of the entire gene family in somatic tissues by mutant analysis has not been possible. Here, we bypassed the reproductive defects of dme mutants to create somatic quadruple homozygous mutants of the entire DME family. dme; ros1; dml2; dml3 (drdd) leaves exhibit hypermethylated genomes compared to both wild-type plants and rdd triple mutants, indicating functional redundancy among all four demethylases. Targets of demethylation include regions co-targeted by RNA-directed DNA methylation and, surprisingly, CG gene body methylation, indicating dynamic methylation at these less-understood sites. Additionally, many tissue-specific methylation differences are absent in drdd, suggesting a role for active demethylation in generating divergent epigenetic states across wild-type tissues. Furthermore, drdd plants display an early flowering phenotype, which is correlated with 5’ hypermethylation and transcriptional down-regulation of FLOWERING LOCUS C. Active DNA demethylation is therefore required for proper methylation patterning across somatic tissues and defines the epigenetic landscape of both intergenic and coding regions.

2021-12-27 | GSE191304 | GEO

Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time [BiSulfite-seq]

2021-12-27 | GSE191006 | GEO

Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-12-27 | GSE191307 | GEO

Flowering Mutant Experiment

Project description:Collection of Flowering mutants Keywords = flowering, growth and development, gene structure and expression Keywords: other

2005-04-09 | GSE2506 | GEO

Targeted DNA demethylation of the Arabidopsis genome using the Human TET1 catalytic domain.

Project description:DNA methylation is important for silencing genes and transposable elements. Changes in DNA methylation can be heritable and thus, the loss or gain of methylation can lead to the formation of stable epialleles. A well characterized example of a stable epiallele in plants is fwa-4, which consists of the loss of DNA cytosine methylation (5mC) in the promoter of the FLOWERING WAGENINGEN (FWA) gene, causing upregulation of FWA and a heritable late flowering phenotype. Here we demonstrate that a fusion between the catalytic domain of the Human demethylase TEN-ELEVEN TRANSLOCATION1 (TET1cd) and an artificial zinc finger (ZF) designed to target the FWA promoter can cause highly efficient targeted demethylation, FWA upregulation, and a heritable late flowering phenotype. Additional ZF-TET1cd fusions designed to target methylated regions of the CACTA1 transposon also caused targeted demethylation and changes in expression. Finally, we have developed a CRISPR/dCAS9 based targeted demethylation system using the TET1cd and a modified SunTag system and demonstrate its ability to target demethylation at and activate the expression of FWA and CACTA1. Our study provides tools for targeted removal of 5mC at specific loci in the genome with high specificity and minimal off-target effects. These tools provide the opportunity to develop new epialleles for traits of interest, and to reactivate expression of previously silenced genes, transgenes, or transposons.

2018-02-18 | GSE109115 | GEO

Flowering Mutant Experiment

Project description:Collection of Flowering mutants Keywords = flowering, growth and development, gene structure and expression

2010-06-10 | E-GEOD-2506 | biostudies-arrayexpress

Widespread endogenous retrotransposition generates somatic genetic mosaicism during human development

Project description:Widespread endogenous retrotransposition generates somatic genetic mosaicism during human development

| PRJEB9178 | ENA

Tet proteins in DNA demethylation and cell fate restriction

Project description:DNA methylation at 5-position of cytosine (5mC) is one of the best studied epigenetic modifications that plays important roles in diverse biological processes. Iterative oxidation of 5mC by the Ten-eleven translocation (Tet) family of proteins generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), which can be further processed by DNA repair proteins leading to DNA demethylation. Functional characterization of the Tet proteins has been complicated by the redundancy between the three Tet proteins. Using the CRISPR/Cas9 technology, we have generated mouse embryonic stem cells (ESCs) deficient for all three Tet proteins (TKO). Whole genome bisulphite sequencing (WGBS) analysis revealed that Tet-mediated DNA demethylation mainly occurs distal enhancers as well as promoters that significantly overlap with 5hmC, 5fC and 5caC. Characterization of the Tet TKO ESCs revealed a function for Tet proteins in cell fate restriction as Tet TKO ESCs tend to adopt both primed pluripotent stem cell-like state and 2-cell embryo-like state. In addition, Tet TKO ESCs exhibit elongated telomeres. Thus, our study reveals a role of Tet proteins not only in DNA demethylation, but also in cell fate restriction and telomere maintenance. 2 samples for WGBS and 2 samples for RNA-seq

2014-09-22 | E-GEOD-56986 | biostudies-arrayexpress

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